Grand Fir / Snowbrush Microbiome

2024-02-16

Preliminary data exploration

Contaminant ASVs were identified with the prevalence method using the decontam package.

Plant measures overview

Scaled-centered plant ‘health’ measures, broken down by treatment factors.

Model output

Formula: value ~ drought * host * site + (1|block))
effect term estimate std.error statistic df p.value
fixed (Intercept) 0.071 0.280 0.255 5.343 0.808
fixed droughtND -0.017 0.163 -0.106 384.262 0.916
fixed hostCeanothus velutinus -0.522 0.164 -3.190 381.647 0.002
fixed fire_freq 0.104 0.154 0.675 5.360 0.528
fixed droughtND:hostCeanothus velutinus 0.560 0.232 2.412 383.262 0.016
fixed droughtND:fire_freq -0.037 0.089 -0.416 381.323 0.677
fixed hostCeanothus velutinus:fire_freq -0.002 0.090 -0.017 382.464 0.987
fixed droughtND:hostCeanothus velutinus:fire_freq -0.033 0.127 -0.263 382.083 0.793




Inoculum communities overview

Taxonomic overview

Bacteria

Alpha diversity

Effect of Shannon diversity on plant measures

## overall_transformed_plant_value ~ Shannon * host * drought * 
##     inoculum_site + (1 | block)
## <environment: 0x5601b01369d0>
effect group term estimate std.error statistic df p.value
fixed NA (Intercept) -0.819 0.484 -1.694 268.342 0.091
fixed NA Shannon 0.177 0.100 1.775 780.109 0.076
fixed NA hostCeanothus velutinus 2.273 2.532 0.898 780.696 0.369
fixed NA droughtND 0.046 2.327 0.020 779.536 0.984
fixed NA inoculum_site2 0.456 1.895 0.241 780.321 0.810
fixed NA inoculum_site3 1.569 4.454 0.352 780.682 0.725
fixed NA inoculum_site4 1.462 1.848 0.791 780.526 0.429
fixed NA inoculum_site5 4.449 3.412 1.304 780.446 0.193
fixed NA inoculum_site6 4.364 1.829 2.386 781.163 0.017
fixed NA inoculum_siteSterile 4.004 2.605 1.537 780.352 0.125
fixed NA Shannon:hostCeanothus velutinus -0.400 0.419 -0.953 780.740 0.341
fixed NA Shannon:droughtND -0.051 0.404 -0.126 779.252 0.900
fixed NA hostCeanothus velutinus:droughtND 10.860 8.385 1.295 782.221 0.196
fixed NA Shannon:inoculum_site2 -0.052 0.342 -0.152 780.485 0.879
fixed NA Shannon:inoculum_site3 -0.387 0.746 -0.520 780.705 0.603
fixed NA Shannon:inoculum_site4 -0.245 0.349 -0.703 780.601 0.482
fixed NA Shannon:inoculum_site5 -0.748 0.606 -1.236 780.466 0.217
fixed NA Shannon:inoculum_site6 -0.756 0.326 -2.318 781.337 0.021
fixed NA Shannon:inoculum_siteSterile -0.776 0.452 -1.717 780.449 0.086
fixed NA hostCeanothus velutinus:inoculum_site2 -1.587 3.204 -0.495 781.728 0.621
fixed NA hostCeanothus velutinus:inoculum_site3 -4.607 6.361 -0.724 782.858 0.469
fixed NA hostCeanothus velutinus:inoculum_site4 -7.546 4.486 -1.682 781.379 0.093
fixed NA hostCeanothus velutinus:inoculum_site5 -10.835 6.908 -1.569 780.616 0.117
fixed NA hostCeanothus velutinus:inoculum_site6 -20.126 7.710 -2.610 778.552 0.009
fixed NA hostCeanothus velutinus:inoculum_siteSterile -4.124 4.378 -0.942 782.874 0.347
fixed NA droughtND:inoculum_site2 -0.849 3.219 -0.264 777.976 0.792
fixed NA droughtND:inoculum_site3 0.110 5.737 0.019 783.218 0.985
fixed NA droughtND:inoculum_site4 0.927 3.782 0.245 780.024 0.806
fixed NA droughtND:inoculum_site5 -2.156 4.458 -0.484 779.469 0.629
fixed NA droughtND:inoculum_site6 -2.233 3.776 -0.591 779.727 0.555
fixed NA droughtND:inoculum_siteSterile -2.731 4.482 -0.609 778.655 0.542
fixed NA Shannon:hostCeanothus velutinus:droughtND -1.855 1.431 -1.296 782.184 0.195
fixed NA Shannon:hostCeanothus velutinus:inoculum_site2 0.244 0.545 0.448 781.808 0.655
fixed NA Shannon:hostCeanothus velutinus:inoculum_site3 0.799 1.031 0.775 782.885 0.438
fixed NA Shannon:hostCeanothus velutinus:inoculum_site4 1.299 0.756 1.719 781.400 0.086
fixed NA Shannon:hostCeanothus velutinus:inoculum_site5 1.841 1.136 1.620 780.686 0.106
fixed NA Shannon:hostCeanothus velutinus:inoculum_site6 3.330 1.240 2.685 778.493 0.007
fixed NA Shannon:hostCeanothus velutinus:inoculum_siteSterile 0.796 0.731 1.090 782.862 0.276
fixed NA Shannon:droughtND:inoculum_site2 0.174 0.570 0.305 777.990 0.761
fixed NA Shannon:droughtND:inoculum_site3 -0.024 0.977 -0.025 781.714 0.980
fixed NA Shannon:droughtND:inoculum_site4 -0.044 0.665 -0.066 779.789 0.947
fixed NA Shannon:droughtND:inoculum_site5 0.395 0.787 0.502 779.396 0.616
fixed NA Shannon:droughtND:inoculum_site6 0.418 0.678 0.617 779.658 0.538
fixed NA Shannon:droughtND:inoculum_siteSterile 0.554 0.771 0.719 778.585 0.473
fixed NA hostCeanothus velutinus:droughtND:inoculum_site2 -8.856 8.911 -0.994 781.979 0.321
fixed NA hostCeanothus velutinus:droughtND:inoculum_site3 -13.316 11.036 -1.207 783.994 0.228
fixed NA hostCeanothus velutinus:droughtND:inoculum_site4 -5.064 9.701 -0.522 781.885 0.602
fixed NA hostCeanothus velutinus:droughtND:inoculum_site5 -0.503 11.503 -0.044 779.167 0.965
fixed NA hostCeanothus velutinus:droughtND:inoculum_site6 9.731 11.483 0.847 778.849 0.397
fixed NA hostCeanothus velutinus:droughtND:inoculum_siteSterile -8.440 9.784 -0.863 780.605 0.389
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 1.523 1.530 0.996 781.901 0.320
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 2.324 1.858 1.251 783.936 0.211
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 0.760 1.660 0.458 781.800 0.647
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 0.143 1.924 0.074 779.246 0.941
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 -1.561 1.918 -0.814 778.858 0.416
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile 1.366 1.666 0.820 780.518 0.413
ran_pars block sd__(Intercept) 0.400 NA NA NA NA
ran_pars Residual sd__Observation 0.898 NA NA NA NA

Fungi

Alpha diversity

Effect of Shannon diversity on plant measures

## overall_transformed_plant_value ~ Shannon * host * drought * 
##     inoculum_site + (1 | block)
## <environment: 0x5601b01369d0>
effect group term estimate std.error statistic df p.value
fixed NA (Intercept) 0.188 0.339 0.555 61.518 0.581
fixed NA Shannon -0.217 0.217 -0.998 780.047 0.319
fixed NA hostCeanothus velutinus -0.461 0.737 -0.626 779.946 0.532
fixed NA droughtND -0.282 0.608 -0.463 778.006 0.643
fixed NA inoculum_site2 0.040 0.603 0.066 779.498 0.947
fixed NA inoculum_site3 -1.247 0.968 -1.289 779.884 0.198
fixed NA inoculum_site4 0.302 0.389 0.776 778.100 0.438
fixed NA inoculum_site5 -0.513 0.798 -0.644 780.535 0.520
fixed NA inoculum_site6 1.255 0.763 1.646 778.880 0.100
fixed NA inoculum_siteSterile -0.937 0.688 -1.363 779.073 0.173
fixed NA Shannon:hostCeanothus velutinus 0.504 0.547 0.920 780.313 0.358
fixed NA Shannon:droughtND 0.276 0.560 0.492 778.364 0.623
fixed NA hostCeanothus velutinus:droughtND 1.080 1.006 1.074 777.445 0.283
fixed NA Shannon:inoculum_site2 0.312 0.458 0.681 779.891 0.496
fixed NA Shannon:inoculum_site3 0.579 0.631 0.917 780.107 0.359
fixed NA Shannon:inoculum_site4 -0.154 0.428 -0.361 778.880 0.718
fixed NA Shannon:inoculum_site5 0.826 0.639 1.291 780.850 0.197
fixed NA Shannon:inoculum_site6 -0.702 0.574 -1.224 778.945 0.221
fixed NA Shannon:inoculum_siteSterile 0.623 0.570 1.093 779.313 0.275
fixed NA hostCeanothus velutinus:inoculum_site2 0.188 1.381 0.136 780.881 0.891
fixed NA hostCeanothus velutinus:inoculum_site3 2.063 1.320 1.563 780.565 0.118
fixed NA hostCeanothus velutinus:inoculum_site4 1.493 1.172 1.274 779.843 0.203
fixed NA hostCeanothus velutinus:inoculum_site5 0.547 1.865 0.293 779.833 0.769
fixed NA hostCeanothus velutinus:inoculum_site6 -0.222 1.821 -0.122 779.773 0.903
fixed NA hostCeanothus velutinus:inoculum_siteSterile 2.113 1.538 1.374 779.727 0.170
fixed NA droughtND:inoculum_site2 0.026 0.874 0.029 778.029 0.977
fixed NA droughtND:inoculum_site3 0.053 1.385 0.038 754.104 0.970
fixed NA droughtND:inoculum_site4 0.236 0.748 0.315 778.469 0.753
fixed NA droughtND:inoculum_site5 1.296 1.213 1.068 779.489 0.286
fixed NA droughtND:inoculum_site6 -1.108 0.989 -1.121 779.728 0.263
fixed NA droughtND:inoculum_siteSterile -0.112 1.154 -0.097 778.270 0.922
fixed NA Shannon:hostCeanothus velutinus:droughtND -0.998 0.805 -1.240 777.461 0.215
fixed NA Shannon:hostCeanothus velutinus:inoculum_site2 -0.480 0.894 -0.537 781.152 0.592
fixed NA Shannon:hostCeanothus velutinus:inoculum_site3 -1.443 0.887 -1.626 780.757 0.104
fixed NA Shannon:hostCeanothus velutinus:inoculum_site4 -0.867 0.880 -0.985 780.238 0.325
fixed NA Shannon:hostCeanothus velutinus:inoculum_site5 -0.742 1.097 -0.676 780.232 0.499
fixed NA Shannon:hostCeanothus velutinus:inoculum_site6 0.261 1.054 0.247 779.406 0.805
fixed NA Shannon:hostCeanothus velutinus:inoculum_siteSterile -1.493 1.147 -1.301 779.750 0.194
fixed NA Shannon:droughtND:inoculum_site2 -0.129 0.784 -0.165 778.228 0.869
fixed NA Shannon:droughtND:inoculum_site3 -0.260 0.969 -0.268 779.728 0.788
fixed NA Shannon:droughtND:inoculum_site4 0.842 1.185 0.711 779.327 0.478
fixed NA Shannon:droughtND:inoculum_site5 -1.298 1.093 -1.187 779.513 0.235
fixed NA Shannon:droughtND:inoculum_site6 0.823 0.821 1.002 780.023 0.317
fixed NA Shannon:droughtND:inoculum_siteSterile 0.408 1.067 0.382 778.550 0.702
fixed NA hostCeanothus velutinus:droughtND:inoculum_site2 -0.025 1.705 -0.015 778.987 0.988
fixed NA hostCeanothus velutinus:droughtND:inoculum_site3 -1.531 1.746 -0.877 776.619 0.381
fixed NA hostCeanothus velutinus:droughtND:inoculum_site4 -2.530 1.433 -1.765 779.634 0.078
fixed NA hostCeanothus velutinus:droughtND:inoculum_site5 -1.896 2.208 -0.859 780.252 0.391
fixed NA hostCeanothus velutinus:droughtND:inoculum_site6 -0.306 2.078 -0.147 778.371 0.883
fixed NA hostCeanothus velutinus:droughtND:inoculum_siteSterile -2.291 1.949 -1.176 778.956 0.240
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 0.254 1.255 0.203 778.785 0.840
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 1.337 1.214 1.101 783.668 0.271
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 0.768 1.459 0.526 779.898 0.599
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 1.893 1.551 1.221 780.466 0.223
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 -0.172 1.317 -0.130 777.754 0.896
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile 1.751 1.668 1.050 779.048 0.294
ran_pars block sd__(Intercept) 0.438 NA NA NA NA
ran_pars Residual sd__Observation 0.902 NA NA NA NA

AMF

Alpha diversity

Effect of Shannon diversity on plant measures

## overall_transformed_plant_value ~ Shannon * host * drought * 
##     inoculum_site + (1 | block)
## <environment: 0x5601b01369d0>
effect group term estimate std.error statistic df p.value
fixed NA (Intercept) -0.144 0.248 -0.579 135.718 0.564
fixed NA Shannon 0.097 0.171 0.569 284.111 0.570
fixed NA droughtND -0.188 0.369 -0.509 337.141 0.611
fixed NA inoculum_site1 -0.014 0.458 -0.031 341.818 0.975
fixed NA inoculum_site2 0.000 0.658 0.000 281.993 1.000
fixed NA inoculum_site3 -1.135 0.494 -2.297 331.577 0.022
fixed NA inoculum_site4 0.505 0.357 1.415 294.169 0.158
fixed NA inoculum_site5 -0.089 0.617 -0.143 338.737 0.886
fixed NA inoculum_site6 0.665 0.565 1.177 334.193 0.240
fixed NA Shannon:droughtND -0.001 0.238 -0.004 305.542 0.997
fixed NA Shannon:inoculum_site1 0.052 0.283 0.183 342.000 0.855
fixed NA Shannon:inoculum_site2 0.109 0.324 0.337 234.877 0.737
fixed NA Shannon:inoculum_site3 -0.047 0.276 -0.172 310.337 0.864
fixed NA Shannon:inoculum_site4 -0.122 0.250 -0.488 193.801 0.626
fixed NA Shannon:inoculum_site5 0.276 0.344 0.803 341.833 0.422
fixed NA Shannon:inoculum_site6 -0.251 0.315 -0.797 314.869 0.426
fixed NA droughtND:inoculum_site1 0.497 0.689 0.721 330.092 0.472
fixed NA droughtND:inoculum_site2 0.534 1.100 0.485 268.573 0.628
fixed NA droughtND:inoculum_site3 0.294 0.628 0.468 327.612 0.640
fixed NA droughtND:inoculum_site4 -0.451 0.619 -0.729 313.535 0.467
fixed NA droughtND:inoculum_site5 1.476 1.319 1.119 298.718 0.264
fixed NA droughtND:inoculum_site6 -1.149 0.781 -1.470 335.103 0.142
fixed NA Shannon:droughtND:inoculum_site1 -0.264 0.381 -0.693 320.169 0.489
fixed NA Shannon:droughtND:inoculum_site2 -0.255 0.479 -0.533 263.141 0.595
fixed NA Shannon:droughtND:inoculum_site3 0.339 0.360 0.941 294.957 0.348
fixed NA Shannon:droughtND:inoculum_site4 0.197 0.363 0.542 256.625 0.588
fixed NA Shannon:droughtND:inoculum_site5 -0.779 0.589 -1.322 318.767 0.187
fixed NA Shannon:droughtND:inoculum_site6 0.487 0.414 1.178 319.987 0.240
ran_pars block sd__(Intercept) 0.158 NA NA NA NA
ran_pars Residual sd__Observation 0.943 NA NA NA NA

Comparison between inoculum and root communities

Bacteria


Not all taxa in the inoculae were subsequently found in the root samples


Fungi


Not all taxa in the inoculae were subsequently found in the root samples


AMF


Not all taxa in the inoculae were subsequently found in the root samples




Microbial guilds

Bacteria

I couldn’t get a trustworthy annotation of “mutualists” for bacteria, but here are probable pathogens:

## value ~ proportion_pathogen * drought * inoculum_site + (1 | 
##     block)
## <environment: 0x5601ba2fa7c0>
effect term estimate std.error statistic df p.value species
fixed (Intercept) 0.1722 0.6500 0.2649 333.5563 0.7913 Ceanothus
fixed proportion_pathogen -2.5700 1.9957 -1.2878 457.3536 0.1985 Ceanothus
fixed droughtND -0.5303 1.0579 -0.5013 455.0687 0.6164 Ceanothus
fixed inoculum_site2 -0.0868 0.7026 -0.1235 454.5472 0.9017 Ceanothus
fixed inoculum_site3 -0.7702 1.0053 -0.7661 455.4777 0.4440 Ceanothus
fixed inoculum_site4 -0.0589 0.9447 -0.0623 453.7538 0.9503 Ceanothus
fixed inoculum_site5 0.1758 0.8327 0.2111 454.2433 0.8329 Ceanothus
fixed inoculum_site6 -1.2336 1.0233 -1.2054 455.5683 0.2287 Ceanothus
fixed inoculum_siteSterile 1.8420 1.2874 1.4308 456.2794 0.1532 Ceanothus
fixed proportion_pathogen:droughtND 4.3306 3.1467 1.3762 455.0446 0.1694 Ceanothus
fixed proportion_pathogen:inoculum_site2 1.8041 2.0727 0.8704 455.4317 0.3845 Ceanothus
fixed proportion_pathogen:inoculum_site3 1.9558 3.8777 0.5044 455.7795 0.6142 Ceanothus
fixed proportion_pathogen:inoculum_site4 1.8027 2.5595 0.7043 453.5567 0.4816 Ceanothus
fixed proportion_pathogen:inoculum_site5 1.2158 2.6144 0.4651 454.3078 0.6421 Ceanothus
fixed proportion_pathogen:inoculum_site6 4.3705 2.8962 1.5091 455.6029 0.1320 Ceanothus
fixed proportion_pathogen:inoculum_siteSterile -4.5708 3.7119 -1.2314 456.4273 0.2188 Ceanothus
fixed droughtND:inoculum_site2 2.0379 1.1867 1.7173 454.9802 0.0866 Ceanothus
fixed droughtND:inoculum_site3 1.3625 1.4248 0.9563 457.1579 0.3394 Ceanothus
fixed droughtND:inoculum_site4 1.4098 1.3478 1.0460 455.1628 0.2961 Ceanothus
fixed droughtND:inoculum_site5 1.0741 1.4700 0.7307 456.8737 0.4653 Ceanothus
fixed droughtND:inoculum_site6 3.3012 1.3995 2.3588 454.9676 0.0188 Ceanothus
fixed droughtND:inoculum_siteSterile 0.6023 1.7437 0.3454 453.9564 0.7299 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site2 -7.0383 3.5798 -1.9661 454.9522 0.0499 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site3 -5.5899 4.8671 -1.1485 457.3762 0.2514 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site4 -3.9924 3.7044 -1.0777 454.8204 0.2817 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site5 -3.3364 4.7703 -0.6994 456.9057 0.4847 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site6 -10.2991 3.9875 -2.5829 454.8270 0.0101 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_siteSterile -2.7184 5.0102 -0.5426 454.0323 0.5877 Ceanothus
fixed (Intercept) -1.1684 0.6277 -1.8615 278.4272 0.0637 Abies
fixed proportion_pathogen 3.6405 1.9071 1.9089 548.7053 0.0568 Abies
fixed droughtND 0.5966 0.7554 0.7898 549.6276 0.4300 Abies
fixed inoculum_site2 1.9585 0.8394 2.3331 548.2551 0.0200 Abies
fixed inoculum_site3 0.6020 0.7181 0.8383 547.3060 0.4022 Abies
fixed inoculum_site4 1.0022 0.7479 1.3400 547.1173 0.1808 Abies
fixed inoculum_site5 0.3777 0.9512 0.3971 546.8517 0.6915 Abies
fixed inoculum_site6 -0.3107 0.8607 -0.3609 549.1792 0.7183 Abies
fixed inoculum_siteSterile 0.2462 0.9624 0.2558 549.5954 0.7982 Abies
fixed proportion_pathogen:droughtND -2.1615 2.2353 -0.9670 549.6902 0.3340 Abies
fixed proportion_pathogen:inoculum_site2 -5.3043 2.6643 -1.9909 548.3235 0.0470 Abies
fixed proportion_pathogen:inoculum_site3 -3.4311 2.5609 -1.3398 547.3609 0.1809 Abies
fixed proportion_pathogen:inoculum_site4 -2.1426 2.5442 -0.8421 547.1342 0.4001 Abies
fixed proportion_pathogen:inoculum_site5 1.9158 3.9387 0.4864 547.0462 0.6269 Abies
fixed proportion_pathogen:inoculum_site6 1.8835 2.9097 0.6473 549.2818 0.5177 Abies
fixed proportion_pathogen:inoculum_siteSterile -2.1258 3.0883 -0.6884 549.6680 0.4915 Abies
fixed droughtND:inoculum_site2 -0.3348 1.2451 -0.2689 547.5612 0.7881 Abies
fixed droughtND:inoculum_site3 -0.5237 1.0952 -0.4782 551.4256 0.6327 Abies
fixed droughtND:inoculum_site4 0.8235 0.9415 0.8747 546.9998 0.3821 Abies
fixed droughtND:inoculum_site5 -0.0074 1.1616 -0.0063 547.6782 0.9949 Abies
fixed droughtND:inoculum_site6 0.7503 1.3710 0.5472 548.5841 0.5844 Abies
fixed droughtND:inoculum_siteSterile 0.3780 1.4953 0.2528 549.3380 0.8005 Abies
fixed proportion_pathogen:droughtND:inoculum_site2 1.2884 3.6496 0.3530 547.6652 0.7242 Abies
fixed proportion_pathogen:droughtND:inoculum_site3 1.4331 3.7849 0.3786 550.3306 0.7051 Abies
fixed proportion_pathogen:droughtND:inoculum_site4 -0.0528 3.1301 -0.0169 547.1331 0.9866 Abies
fixed proportion_pathogen:droughtND:inoculum_site5 -1.9470 4.3400 -0.4486 547.4146 0.6539 Abies
fixed proportion_pathogen:droughtND:inoculum_site6 -2.6534 4.1681 -0.6366 548.8049 0.5247 Abies
fixed proportion_pathogen:droughtND:inoculum_siteSterile -0.1118 4.4805 -0.0250 549.3584 0.9801 Abies

Fungi

How does the proportion of mutualist fungi relate to indicators of plant health?

In the following figure, the X-axis represents the proportion of fungi that could be identified to a mutualistic guild; the Y-axis represents the value of the various measures of plant success (facets). Y-axis scales vary between facets.

We see an opposite pattern when looking at the proportions of putatively pathogenic fungi

effect term estimate std.error statistic df p.value species
fixed (Intercept) -0.6206 0.2539 -2.4437 55.1101 0.0178 Ceanothus
fixed proportion_pathogen 0.0054 1.5614 0.0035 457.7107 0.9972 Ceanothus
fixed droughtND 0.8428 0.2734 3.0830 455.9070 0.0022 Ceanothus
fixed inoculum_site2 0.3041 0.2835 1.0727 457.0738 0.2840 Ceanothus
fixed inoculum_site3 0.1344 0.2990 0.4496 457.2861 0.6532 Ceanothus
fixed inoculum_site4 0.3135 0.2792 1.1230 455.4997 0.2620 Ceanothus
fixed inoculum_site5 0.5478 0.2922 1.8745 454.2481 0.0615 Ceanothus
fixed inoculum_site6 0.5105 0.4132 1.2354 457.6179 0.2173 Ceanothus
fixed inoculum_siteSterile 0.6209 0.3546 1.7512 455.3257 0.0806 Ceanothus
fixed proportion_pathogen:droughtND 0.1774 1.7416 0.1018 457.7728 0.9189 Ceanothus
fixed proportion_pathogen:inoculum_site2 0.5303 1.9913 0.2663 457.9753 0.7901 Ceanothus
fixed proportion_pathogen:inoculum_site3 -2.1050 1.9835 -1.0613 457.9997 0.2891 Ceanothus
fixed proportion_pathogen:inoculum_site4 1.1373 1.9865 0.5725 456.9036 0.5673 Ceanothus
fixed proportion_pathogen:inoculum_site5 -0.0184 1.6735 -0.0110 456.0497 0.9912 Ceanothus
fixed proportion_pathogen:inoculum_site6 -1.7846 2.6850 -0.6647 457.9989 0.5066 Ceanothus
fixed proportion_pathogen:inoculum_siteSterile -2.9619 2.0318 -1.4578 456.4852 0.1456 Ceanothus
fixed droughtND:inoculum_site2 0.0832 0.3752 0.2217 457.0510 0.8247 Ceanothus
fixed droughtND:inoculum_site3 -0.9731 0.3917 -2.4845 457.1136 0.0133 Ceanothus
fixed droughtND:inoculum_site4 0.3713 0.3656 1.0157 455.2958 0.3103 Ceanothus
fixed droughtND:inoculum_site5 0.0142 0.3787 0.0376 455.0280 0.9700 Ceanothus
fixed droughtND:inoculum_site6 -0.3019 0.4833 -0.6246 457.6711 0.5325 Ceanothus
fixed droughtND:inoculum_siteSterile -0.6398 0.4347 -1.4717 455.0357 0.1418 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site2 4.8521 5.9000 0.8224 457.9850 0.4113 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site3 2.6732 2.1909 1.2201 457.9916 0.2230 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site4 -6.0638 6.3317 -0.9577 457.6471 0.3387 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site5 0.2554 4.0843 0.0625 457.7288 0.9502 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_site6 0.1759 3.4237 0.0514 457.5146 0.9590 Ceanothus
fixed proportion_pathogen:droughtND:inoculum_siteSterile 1.8355 4.7671 0.3850 457.9841 0.7004 Ceanothus
fixed (Intercept) 0.1478 0.2478 0.5964 13.8739 0.5605 Abies
fixed proportion_pathogen -1.9751 0.9250 -2.1354 548.8206 0.0332 Abies
fixed droughtND 0.0247 0.2145 0.1154 547.9589 0.9082 Abies
fixed inoculum_site2 0.0796 0.2039 0.3901 547.6619 0.6966 Abies
fixed inoculum_site3 -0.7450 0.2235 -3.3342 547.9680 0.0009 Abies
fixed inoculum_site4 0.2825 0.1956 1.4440 546.2481 0.1493 Abies
fixed inoculum_site5 0.3839 0.2171 1.7683 547.0385 0.0776 Abies
fixed inoculum_site6 -0.0544 0.2123 -0.2563 547.8979 0.7978 Abies
fixed inoculum_siteSterile -0.5612 0.1991 -2.8189 546.2514 0.0050 Abies
fixed proportion_pathogen:droughtND 0.9260 1.1581 0.7995 549.7808 0.4243 Abies
fixed proportion_pathogen:inoculum_site2 4.1635 3.4089 1.2214 549.5705 0.2225 Abies
fixed proportion_pathogen:inoculum_site3 2.6887 1.3328 2.0173 549.5680 0.0441 Abies
fixed proportion_pathogen:inoculum_site4 -5.2127 2.3490 -2.2191 546.9085 0.0269 Abies
fixed proportion_pathogen:inoculum_site5 1.4309 1.0617 1.3477 548.3326 0.1783 Abies
fixed proportion_pathogen:inoculum_site6 1.7646 1.1940 1.4779 549.8710 0.1400 Abies
fixed proportion_pathogen:inoculum_siteSterile 1.8120 0.9748 1.8588 547.3155 0.0636 Abies
fixed droughtND:inoculum_site2 -0.1984 0.2886 -0.6874 548.2016 0.4921 Abies
fixed droughtND:inoculum_site3 -0.1630 0.3276 -0.4976 550.8398 0.6190 Abies
fixed droughtND:inoculum_site4 0.3025 0.2972 1.0176 546.9898 0.3093 Abies
fixed droughtND:inoculum_site5 -0.4240 0.2957 -1.4337 547.2791 0.1522 Abies
fixed droughtND:inoculum_site6 -0.0196 0.2954 -0.0662 548.2796 0.9472 Abies
fixed droughtND:inoculum_siteSterile 0.4723 0.2999 1.5750 547.4331 0.1158 Abies
fixed proportion_pathogen:droughtND:inoculum_site2 -2.0132 3.5833 -0.5618 550.2289 0.5745 Abies
fixed proportion_pathogen:droughtND:inoculum_site3 -0.8609 1.7701 -0.4863 551.5755 0.6269 Abies
fixed proportion_pathogen:droughtND:inoculum_site4 83.6612 27.2828 3.0664 548.5544 0.0023 Abies
fixed proportion_pathogen:droughtND:inoculum_site5 3.2732 1.9160 1.7083 548.7870 0.0881 Abies
fixed proportion_pathogen:droughtND:inoculum_site6 -0.4152 1.5803 -0.2627 550.2599 0.7929 Abies
fixed proportion_pathogen:droughtND:inoculum_siteSterile -5.4061 2.1744 -2.4862 549.0231 0.0132 Abies
fixed (Intercept) -0.8022 0.3399 -2.3599 161.0649 0.0195 Ceanothus
fixed proportion_mutualist 0.3218 0.5106 0.6302 457.5517 0.5289 Ceanothus
fixed droughtND 0.6591 0.4237 1.5554 456.3827 0.1205 Ceanothus
fixed inoculum_site2 0.3828 0.3705 1.0332 456.4647 0.3021 Ceanothus
fixed inoculum_site3 -0.4801 0.3963 -1.2115 456.6666 0.2263 Ceanothus
fixed inoculum_site4 0.9985 0.6939 1.4390 457.2532 0.1508 Ceanothus
fixed inoculum_site5 0.6621 0.3773 1.7547 457.9637 0.0800 Ceanothus
fixed inoculum_site6 0.2690 0.3783 0.7111 455.7693 0.4774 Ceanothus
fixed inoculum_siteSterile -0.7110 0.8686 -0.8186 456.9198 0.4135 Ceanothus
fixed proportion_mutualist:droughtND 0.9691 0.9799 0.9890 457.2576 0.3232 Ceanothus
fixed proportion_mutualist:inoculum_site2 0.7436 1.1344 0.6555 457.6023 0.5125 Ceanothus
fixed proportion_mutualist:inoculum_site3 0.8005 0.6597 1.2134 457.3896 0.2256 Ceanothus
fixed proportion_mutualist:inoculum_site4 -1.3078 1.5481 -0.8448 457.4213 0.3987 Ceanothus
fixed proportion_mutualist:inoculum_site5 0.3756 1.6375 0.2294 457.8880 0.8187 Ceanothus
fixed proportion_mutualist:inoculum_site6 1.0091 1.4034 0.7190 457.2809 0.4725 Ceanothus
fixed proportion_mutualist:inoculum_siteSterile 1.6008 1.6381 0.9772 457.0660 0.3290 Ceanothus
fixed droughtND:inoculum_site2 0.3825 0.5067 0.7549 457.2408 0.4507 Ceanothus
fixed droughtND:inoculum_site3 0.0189 0.5346 0.0354 457.3001 0.9718 Ceanothus
fixed droughtND:inoculum_site4 -0.7769 0.8372 -0.9280 456.4201 0.3539 Ceanothus
fixed droughtND:inoculum_site5 0.4308 0.5170 0.8333 457.4848 0.4051 Ceanothus
fixed droughtND:inoculum_site6 -0.5954 0.5138 -1.1587 457.4218 0.2472 Ceanothus
fixed droughtND:inoculum_siteSterile 1.0775 1.0150 1.0616 455.7404 0.2890 Ceanothus
fixed proportion_mutualist:droughtND:inoculum_site2 -1.4437 1.6302 -0.8856 457.9597 0.3763 Ceanothus
fixed proportion_mutualist:droughtND:inoculum_site3 -1.6146 1.1588 -1.3933 457.9576 0.1642 Ceanothus
fixed proportion_mutualist:droughtND:inoculum_site4 1.0803 1.8058 0.5982 455.7461 0.5500 Ceanothus
fixed proportion_mutualist:droughtND:inoculum_site5 -2.1865 1.9014 -1.1499 457.7228 0.2508 Ceanothus
fixed proportion_mutualist:droughtND:inoculum_site6 2.9041 1.8986 1.5296 456.9243 0.1268 Ceanothus
fixed proportion_mutualist:droughtND:inoculum_siteSterile -2.9672 1.9533 -1.5191 457.0488 0.1294 Ceanothus
fixed (Intercept) -0.5757 0.3669 -1.5690 62.0891 0.1217 Abies
fixed proportion_mutualist 0.6794 0.4248 1.5995 549.1340 0.1103 Abies
fixed droughtND -0.0667 0.4641 -0.1437 549.0047 0.8858 Abies
fixed inoculum_site2 0.8297 0.4183 1.9837 548.5466 0.0478 Abies
fixed inoculum_site3 -0.0018 0.3381 -0.0053 548.3096 0.9958 Abies
fixed inoculum_site4 0.3730 0.4131 0.9029 547.3019 0.3670 Abies
fixed inoculum_site5 1.2056 0.3598 3.3509 547.8740 0.0009 Abies
fixed inoculum_site6 0.3313 0.3982 0.8319 547.6122 0.4058 Abies
fixed inoculum_siteSterile -0.3805 0.3705 -1.0268 548.1281 0.3050 Abies
fixed proportion_mutualist:droughtND 0.1357 0.6173 0.2198 549.3408 0.8261 Abies
fixed proportion_mutualist:inoculum_site2 -0.7573 0.6259 -1.2100 548.8757 0.2268 Abies
fixed proportion_mutualist:inoculum_site3 -0.6754 0.6565 -1.0287 548.4715 0.3041 Abies
fixed proportion_mutualist:inoculum_site4 -0.1363 0.5557 -0.2453 547.3979 0.8063 Abies
fixed proportion_mutualist:inoculum_site5 -2.6207 1.1763 -2.2280 548.2486 0.0263 Abies
fixed proportion_mutualist:inoculum_site6 -0.0784 0.7127 -0.1100 547.8722 0.9125 Abies
fixed proportion_mutualist:inoculum_siteSterile 0.2307 0.5512 0.4186 548.2973 0.6757 Abies
fixed droughtND:inoculum_site2 0.4104 0.5680 0.7226 547.7570 0.4702 Abies
fixed droughtND:inoculum_site3 -0.2531 0.5176 -0.4891 551.7549 0.6250 Abies
fixed droughtND:inoculum_site4 3.4378 0.9621 3.5732 549.2918 0.0004 Abies
fixed droughtND:inoculum_site5 -0.4996 0.5684 -0.8791 547.4239 0.3797 Abies
fixed droughtND:inoculum_site6 0.4695 0.5484 0.8561 548.0989 0.3923 Abies
fixed droughtND:inoculum_siteSterile 0.7380 0.5395 1.3680 548.5313 0.1719 Abies
fixed proportion_mutualist:droughtND:inoculum_site2 -1.0961 0.8196 -1.3373 548.0729 0.1817 Abies
fixed proportion_mutualist:droughtND:inoculum_site3 0.8786 1.0742 0.8180 206.1281 0.4143 Abies
fixed proportion_mutualist:droughtND:inoculum_site4 -3.2430 1.1791 -2.7503 549.2426 0.0062 Abies
fixed proportion_mutualist:droughtND:inoculum_site5 2.0835 1.3407 1.5540 547.9146 0.1208 Abies
fixed proportion_mutualist:droughtND:inoculum_site6 -1.0679 0.8860 -1.2053 547.7981 0.2286 Abies
fixed proportion_mutualist:droughtND:inoculum_siteSterile -0.9759 0.9337 -1.0452 548.9449 0.2964 Abies




Beta-Diversity

Bacteria

## PermANOVA run without outlier Sterile-inoculum root samples...
term df SumOfSqs R2 statistic p.value
host 1 3.8414120 0.0687480 11.063965 0.001
fire_freq 1 1.7434756 0.0312022 5.021527 0.001
drought 1 0.8088162 0.0144750 2.329538 0.001
host:fire_freq 1 0.7153777 0.0128028 2.060418 0.002
host:drought 1 0.7562988 0.0135351 2.178278 0.002
fire_freq:drought 1 0.3814427 0.0068265 1.098624 0.234
host:fire_freq:drought 1 0.4106606 0.0073494 1.182777 0.162
Residual 136 47.2192419 0.8450610 NA NA
Total 143 55.8767255 1.0000000 NA NA

Fungi

## PermANOVA run without outlier Sterile-inoculum root samples...
term df SumOfSqs R2 statistic p.value
host 1 1.9352113 0.0300393 4.6753844 0.001
fire_freq 1 3.4231420 0.0531356 8.2701587 0.001
drought 1 0.5712680 0.0088675 1.3801580 0.113
host:fire_freq 1 0.9705051 0.0150646 2.3446971 0.003
host:drought 1 0.3803731 0.0059043 0.9189645 0.583
fire_freq:drought 1 0.5128794 0.0079612 1.2390938 0.202
host:fire_freq:drought 1 0.3369443 0.0052302 0.8140424 0.746
Residual 136 56.2924276 0.8737973 NA NA
Total 143 64.4227507 1.0000000 NA NA

AMF

## PermANOVA run without outlier Sterile-inoculum root samples...
term df SumOfSqs R2 statistic p.value
inoculum_site 6 6.9907731 0.2129210 2.9819777 0.001
drought 1 0.3007071 0.0091588 0.7696159 0.783
inoculum_site:drought 6 2.0978089 0.0638939 0.8948394 0.794
Residual 60 23.4434120 0.7140263 NA NA
Total 73 32.8327011 1.0000000 NA NA




Important Taxa

These taxa were identified by both Random Forest models and corncob as being important predictors of the various experimental conditions & had significant differential abundance between levels of those variables

Bacteria

Differential Abundance

Relative Abundances of ‘important’ taxa in root samples

Fungi

Differential Abundance

No fungal taxa were found to have significant differential abundance between drought levels

Relative Abundances of ‘important’ taxa in root samples


AMF

Differential Abundance

No fungal taxa were found to have significant differential abundance between drought levels

Relative Abundances of ‘important’ taxa in root samples




Phylogenetic properties

Bacteria

  • Still kind of messy
  • What specific questions do we need to address with this?

Fungi

  • Phylogenetic dispersion is tricky with ITS markers :(
  • Could try GhostTree for fungi of interest that come up as ‘unknown’




Network properties

Selected network attributes

Network properties vs Plant Health

(Composite scaled-centered plant health measures)

## plant_health_indicator ~ species * kingdom * (n_vertices + n_edges + 
##     mean_dist + mean_betweenness + mean_closeness + global_effic + 
##     clustering_coeficient + max_degree)
term estimate std.error statistic p.value
(Intercept) -0.3395498 1.1487865 -0.2955726 0.7675797
speciesSnowbrush 0.7900657 1.0513415 0.7514834 0.4524286
kingdomBacteria 0.7824899 1.1780848 0.6642051 0.5066169
kingdomFungi -0.1216436 0.9017750 -0.1348935 0.8927063
n_vertices 0.0336583 0.0182490 1.8443884 0.0652382
n_edges -0.0062740 0.0025937 -2.4189740 0.0156314
mean_dist 0.1045359 0.2745054 0.3808154 0.7033708
mean_betweenness -0.0093545 0.0130007 -0.7195376 0.4718733
mean_closeness -0.4507788 1.6083510 -0.2802739 0.7792893
global_effic 0.0709782 0.8650863 0.0820475 0.9346151
clustering_coeficient 0.5004481 0.2923773 1.7116517 0.0870780
max_degree -0.0027581 0.0111646 -0.2470390 0.8048972
speciesSnowbrush:kingdomBacteria -1.9196549 1.3356853 -1.4372060 0.1507777
speciesSnowbrush:kingdomFungi NA NA NA NA
speciesSnowbrush:n_vertices -0.0277443 0.0162003 -1.7125829 0.0869064
speciesSnowbrush:n_edges 0.0056234 0.0022927 2.4526859 0.0142435
speciesSnowbrush:mean_dist -0.1783225 0.2516005 -0.7087527 0.4785404
speciesSnowbrush:mean_betweenness 0.0069343 0.0117019 0.5925841 0.5535102
speciesSnowbrush:mean_closeness 0.0505584 1.5604034 0.0324008 0.9741548
speciesSnowbrush:global_effic -0.2616951 0.7889638 -0.3316946 0.7401461
speciesSnowbrush:clustering_coeficient -0.4328359 0.2784180 -1.5546258 0.1201548
speciesSnowbrush:max_degree 0.0010310 0.0103857 0.0992750 0.9209275
kingdomBacteria:n_vertices -0.0412751 0.0191732 -2.1527432 0.0314290
kingdomFungi:n_vertices -0.0131249 0.0107850 -1.2169553 0.2237297
kingdomBacteria:n_edges 0.0070137 0.0038534 1.8201147 0.0688544
kingdomFungi:n_edges 0.0016993 0.0014452 1.1758683 0.2397532
kingdomBacteria:mean_dist -0.1393771 0.2812262 -0.4956049 0.6202143
kingdomFungi:mean_dist 0.0793556 0.2149002 0.3692673 0.7119580
kingdomBacteria:mean_betweenness 0.0127671 0.0132366 0.9645311 0.3348678
kingdomFungi:mean_betweenness 0.0051542 0.0075743 0.6804893 0.4962542
kingdomBacteria:mean_closeness 0.2616321 1.6248329 0.1610209 0.8720892
kingdomFungi:mean_closeness 0.8705704 1.2202795 0.7134189 0.4756495
kingdomBacteria:global_effic -0.5859759 0.9583746 -0.6114268 0.5409696
kingdomFungi:global_effic 0.1112992 0.6967625 0.1597377 0.8730999
kingdomBacteria:clustering_coeficient -0.0612045 0.3475835 -0.1760857 0.8602401
kingdomFungi:clustering_coeficient -0.3444858 0.2348469 -1.4668530 0.1425348
kingdomBacteria:max_degree 0.0169423 0.0144749 1.1704638 0.2419197
kingdomFungi:max_degree 0.0104688 0.0062428 1.6769499 0.0936703
speciesSnowbrush:kingdomBacteria:n_vertices 0.0342394 0.0190432 1.7979889 0.0722927
speciesSnowbrush:kingdomFungi:n_vertices NA NA NA NA
speciesSnowbrush:kingdomBacteria:n_edges -0.0036401 0.0041559 -0.8758998 0.3811640
speciesSnowbrush:kingdomFungi:n_edges NA NA NA NA
speciesSnowbrush:kingdomBacteria:mean_dist 0.4252445 0.2905229 1.4637210 0.1433889
speciesSnowbrush:kingdomFungi:mean_dist NA NA NA NA
speciesSnowbrush:kingdomBacteria:mean_betweenness -0.0169793 0.0126385 -1.3434610 0.1792379
speciesSnowbrush:kingdomFungi:mean_betweenness NA NA NA NA
speciesSnowbrush:kingdomBacteria:mean_closeness 2.0054281 1.7097727 1.1729209 0.2409331
speciesSnowbrush:kingdomFungi:mean_closeness NA NA NA NA
speciesSnowbrush:kingdomBacteria:global_effic 2.4227245 1.3447266 1.8016483 0.0717145
speciesSnowbrush:kingdomFungi:global_effic NA NA NA NA
speciesSnowbrush:kingdomBacteria:clustering_coeficient -0.6159688 0.4870200 -1.2647710 0.2060648
speciesSnowbrush:kingdomFungi:clustering_coeficient NA NA NA NA
speciesSnowbrush:kingdomBacteria:max_degree -0.0157006 0.0160879 -0.9759266 0.3291900
speciesSnowbrush:kingdomFungi:max_degree NA NA NA NA


_____


Soil chemistry

Overview of soil properties for each inoculum source:

Testing for significant differences between the samples…

Here are the soil properties that differ significantly between inoculum sources. Sterile inoculum soils are set as the intercept. The stats below pretty nicely reflect the obvious patterns in the overall figure.
term estimate std.error statistic p.value
Mn 1.248 0.268 4.658 0.000
NH4 0.770 0.268 2.875 0.004
Fe:inoc_site1 1.516 0.328 4.618 0.000
K:inoc_site1 0.904 0.328 2.753 0.006
NO3:inoc_site1 -0.793 0.328 -2.417 0.016
TKN:inoc_site1 0.735 0.328 2.240 0.026
Zn:inoc_site1 1.160 0.328 3.536 0.000
Fe:inoc_site2 0.831 0.328 2.532 0.012
K:inoc_site2 0.801 0.328 2.440 0.015
Mn:inoc_site2 -1.081 0.328 -3.294 0.001
TKN:inoc_site2 0.660 0.328 2.010 0.045
Mn:inoc_site3 -1.526 0.328 -4.648 0.000
NH4:inoc_site3 -0.976 0.328 -2.973 0.003
Zn:inoc_site3 -0.693 0.328 -2.112 0.035
C:N:inoc_site4 -0.893 0.328 -2.721 0.007
EC:inoc_site4 -1.026 0.328 -3.127 0.002
Mn:inoc_site4 -1.349 0.328 -4.110 0.000
B:inoc_site5 1.369 0.328 4.171 0.000
Ca:inoc_site5 1.192 0.328 3.631 0.000
K:inoc_site5 0.683 0.328 2.080 0.038
Mg:inoc_site5 0.682 0.328 2.078 0.039
Mn:inoc_site5 -1.099 0.328 -3.350 0.001
NO3:inoc_site5 1.854 0.328 5.649 0.000
TKN:inoc_site5 1.022 0.328 3.114 0.002
Zn:inoc_site5 1.448 0.328 4.412 0.000
B:inoc_site6 0.918 0.328 2.798 0.005
Mn:inoc_site6 -1.535 0.328 -4.678 0.000
NH4:inoc_site6 -0.754 0.328 -2.299 0.022
NO3:inoc_site6 1.273 0.328 3.880 0.000
Zn:inoc_site6 1.290 0.328 3.932 0.000